[BioC] Ruuid had non-zero exit status

Herve Pages hpages at fhcrc.org
Tue Jun 13 22:37:10 CEST 2006


Hi Zong-Pei,

Since you are using the same OS and gcc version than our test machine:
  http://bioconductor.org/checkResults/1.8/churchill-NodeInfo.html
I'm wondering why gcc is not using the same flags on your system!
You have:

    gcc -I/package/R/2.3.1/lib/R/include -I/package/R/2.3.1/lib/R/include \
      -I/usr/local/include -I/ usr/local/include/glib-2.0 \
      -I/usr/local/lib/glib-2.0/include -DHAVE_UNISTD_H=1 -fPIC -O2 \
      -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -c Rinit.c -o Rinit.o

but we have:

    gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include \
      -I/usr/local/include -I/usr/local/include/glib-2.0 \
      -I/usr/local/lib/glib-2.0/include -DHAVE_UNISTD_H=1 -fPIC -g -O2 \
      -std=gnu99 -Wall -c Rinit.c -o Rinit.o

Could it be possible that your gcc is a 64-bit version? (ours is a 
32-bit version,
even if the OS is 64-bit). To figure out:

    hpages at churchill:~> which gcc
    /usr/local/bin/gcc
    hpages at churchill:~> file /usr/local/bin/gcc
    /usr/local/bin/gcc: ELF 32-bit MSB executable SPARC Version 1,
    dynamically linked, not stripped

Best,

H.

zph at herald.ox.ac.uk wrote:
> Hi,
>
> I must say that the same gcc and glib2 work fine to compile
> R pre-2.3.x
>
> Here're some additional information:
>
> zph at orac [zph]$ gcc --version
> gcc (GCC) 3.4.2
> Copyright (C) 2004 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions. There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
> PURPOSE.
>
> zph at orac [zph]$ pkg-config --modversion glib-2.0
> 2.6.2
>
> Regards,
>
> Zong-Pei
> Dear ,
>
>
> Regards,
>
> Zong-Pei
> -------------------------------------
> Dr Zong-Pei Han
> UNIX Systems Administrator
> Computational Biology Research Group
> University of Oxford
>
> Tel: 01865 285731
> http://www.compbio.ox.ac.uk/
> -------------------------------------
>
>
> On Mon, 12 Jun 2006, Seth Falcon wrote:
> Date: Mon, 12 Jun 2006 08:35:39 -0700
> From: Seth Falcon <sfalcon at fhcrc.org>
> To: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Ruuid had non-zero exit status
>
> zph at herald.ox.ac.uk writes:
>
>> Hope someone can point the right direction to solve
>> the problem. Thanks.
>
> Hmm, what version of glib-2.0 do you have?
>
> Try: pkg-config --modversion glib-2.0
>
> What version of gcc?
>
> + seth
>
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Hervé Pagès
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